Small organic molecules are often used to modulate the function of disease-related proteins and thereby promote and restore human health. In the chemical genetics approach, libraries of small molecules are used systematically to perturb and thereby elucidate protein function. When the protein of interest is a cause for human disease, the hit from the screening in biological assays may also find its use in therapeutic remedies. If chemical genetic screens are to result in the discovery of new small molecules with powerful physiological effects, libraries of unique and diverse small molecules are desired. Ideally, a library of small molecules should be able to perturb most of the proteins in humans, but this ideal chemical library does not yet exist. As a step toward this goal, diversity-oriented synthesis (DOS) has emerged as a new paradigm. The goal in DOS is to generate an array of small molecules that differ in their three-dimensional scaffolds;however, gaining access to scaffold diversity has proven to be more challenging than creating a library of compounds derived from one scaffold, as in combinatorial chemistry. In this proposal we analyze the current state of DOS and propose a powerful mechanism for it: combinatorial scaffolding. In the combinatorial scaffolding strategy a multiplicative increase in the number of scaffolds is achieved with an additive increase in the number of reaction conditions. To achieve combinatorial scaffolding, the development of phosphine-catalyzed allenoate annulations is proposed. When the proposed annulations are performed on the resin-bound allenoates, a library of compounds with 53 different scaffolds will be generated. Since the products from the proposed library contain at least one variable substituent, the project will produce a library of libraries. These libraries will be submitted to the NIH Molecular Libraries Small-Molecule Repository (MLSMR) for high-throughput biological screening. The process of developing the proposed chemical synthesis has already produced 171 model compounds. Preliminary assays using these compounds have resulted in the discovery of small molecule enzyme inhibitors for GGTase I, FTase, palmitoyltransferase, and phosphatases, as well as several more chemicals with interesting biological activities. The four enzymes are implicated in diverse human disorders, such as cancer, heart diseases, diabetes, and Alzheimer's;therefore, the small molecule ligands we discovered in our initial library have significant medical implications.